File	Date	Author	Commit
data	2012-08-03	Daniel Standage	[3b899e] Merge branch 'master' of ssh://parseval.git.sou...
docs	2012-05-16	Daniel Standage	[da44b0] Updated docs
inc	2012-08-02	Daniel Standage	[953c37] Substantial refactoring
src	2013-07-24	Daniel Standage	[5cf772] Fix for GT 1.5.1 compatibility
CONTRIBUTORS	2012-08-03	Daniel Standage	[aa5ba7] Corrected license and attributions
LICENSE	2012-08-03	Daniel Standage	[aa5ba7] Corrected license and attributions
README	2012-08-03	Daniel Standage	[aa5ba7] Corrected license and attributions
makefile	2012-08-02	Daniel Standage	[953c37] Substantial refactoring

Read Me

This directory contains the source code for ParsEval version 0.9.1.

Copyright (c) 2010-2012, Daniel S. Standage and CONTRIBUTORS
See CONTRIBUTORS and LICENSE or http://parseval.sourceforge.net/license.txt for
details.

ParsEval is a program for comparing distinct sets of gene structure annotations
for the same sequence(s). This program calculates and reports a rich set of
comparison statistics, both at the level of individual gene loci as well as at
the level of entire sequences.

Please cite ParsEval as follows.

Standage, Daniel S. and Volker P. Brendel (2012) ParsEval: parallel comparison
and analysis of gene structure annotations. BMC Bioinformatics, 13:187.


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Installation instructions for the impatient
--------------------------------------------------------------------------------
If you have root access to a Linux system, chances are you can simply run the
commands below to install ParsEval. I provide commands as would be run in the
Ubuntu distribution. Similar commands should be available for any other Linux
distribution. If you're not running Linux, or if you run into any problems
following these commands, you should probably take some time to read through the
rest of the installation instructions before proceeding.

  # Run as root
  sudo bash

  # System environment configuration (platform-dependent)
  # See `docs' directory for platform-specific configuration instructions
  echo $PATH | grep /usr/local/bin || (export PATH=/usr/local/bin:$PATH && /
       echo 'export PATH=/usr/local/bin:$PATH' >> /etc/bash.bashrc)
  test -d /usr/local/src || mkdir -p /usr/local/src
  grep '/usr/local/lib' /etc/ld.so.conf || /
       (echo '/usr/local/lib' >> /etc/ld.so.conf && ldconfig)
  apt-get install -y build-essential git libcairo2-dev libncurses5-dev

  # Install GenomeTools and ParsEval (platform-independent)
  cd /usr/local/src
  git clone git://genometools.org/genometools.git
  cd genometools
  make 64bit=yes
  make install

  cd /usr/local/src
  git clone git://parseval.git.sourceforge.net/gitroot/parseval/parseval
  cd parseval
  make 64bit=yes
  make install

  # Test ParsEval: print usage statement
  parseval -h


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Prerequisites
--------------------------------------------------------------------------------
In principle, ParsEval should compile and run on any POSIX-compliant UNIX system
(Linux, Mac OS X, Cygwin), although in practice, it has only been tested on
Linux and Mac systems. Native Windows support is not anticipated any time soon.
The ParsEval developers have made an effort to minimize dependency on external
software, but compiling and installing does require a few prerequisites.

First, the system must include common Unix tools for building software:
specifically, GNU make (version 3.80 or later) and a C compiler with OpenMP
support (e.g. GCC 4.2 or higher). Additionally, the system must have the
GenomeTools library installed (see http://genometools.org/ for download and
installation instructions). To fully take advantage of the graphics capabilities
provided by GenomeTools, the system must also have an installation of the Cairo
graphics library (see the GenomeTools documentation).


--------------------------------------------------------------------------------
Compiling and installing
--------------------------------------------------------------------------------
It is generally assumed that the user will follow standard Linux/Unix procedures
when downloading, compiling, and installing the GenomeTools prerequisite. The
default install directory is `/usr/local', which means that we assume the
GenomeTools source code has been placed in `/usr/local/src/', the binaries have
been installed in `/usr/local/bin', the shared libraries have been installed in
`/usr/local/lib', and so forth.

If this is the case, then the installation procedure described above should work
just fine. From the directory containing the ParsEval source code distribution,
enter the following commands.

  make
  make install # requires root access

If you have some reason to install GenomeTools in some other directory (e.g.
if you don't have permissions to modify `/usr/local'), this should not be a
problem for ParsEval. You must simply tell ParsEval where to find GenomeTools.
For example, if you installed GenomeTools in `/home/alice/local', then you must
indicate this fact when compiling ParsEval.

The following `make' options are available if you encounter any problems during
installation or if you want to customize your installation.

  - 64bit=yes        if you want compile for a 64-bit architecture
  - cairo=no         if your system does not have Cairo graphics libraries
                     installed (you will not be able to generate graphics)
  - GT_INSTALL_DIR=? if you did not install GenomeTools in `/usr/local'
  - GT_COMPILE_DIR=? if you did not download and compile GenomeTools in
                     `/usr/local/src/genometools'
  - prefix=?         to install ParsEval in a directory other than
                     `/usr/local' (e.g. if you do not have admin privileges)

For example, if I need to install GenomeTools and ParsEval in my home directory
(`/home/alice'), then I could do something like this.

  test -d /home/alice/local/src || mkdir -p /home/alice/local/src

  cd /home/alice/local/src
  git clone git://genometools.org/genometools.git
  cd genometools
  make prefix=/home/alice/local 64bit=yes
  make prefix=/home/alice/local 64bit=yes install

  cd /home/alice/local/src
  git clone git://parseval.git.sourceforge.net/gitroot/parseval/parseval
  cd parseval
  make prefix=/home/alice/local GT_INSTALL_DIR=/home/alice/local /
       GT_COMPILE_DIR=/home/alice/local/src/genometools 64bit=yes
  make prefix=/home/alice/local GT_INSTALL_DIR=/home/alice/local /
       GT_COMPILE_DIR=/home/alice/local/src/genometools 64bit=yes install

Remember that if you install the GenomeTools library in a non-standard location,
you will need to make sure that the ParsEval program can find that library at
runtime. This can be done on a temporary basis using the `LD_LIBRARY_PATH'
environmental variable or on a permanent system-wide basis using the `ldconfig'
command.

Although the `/usr/local' directory is the standard install location for 3rd
party libraries, on some distributions this directory is not pre-configured.
If you use the default install locations and still run into problems, make sure
that `/usr/local/bin' is in your path (using the `export' or `setenv' commands)
and that `/usr/local/lib' is in the LD path (using the `ldconfig' command).


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Running ParsEval
--------------------------------------------------------------------------------
Invoking `parseval -h' will print a helpful usage statement to the terminal.
Also, see data/benchmarks/README for several examples demonstrating ParsEval's
features.


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Contact
--------------------------------------------------------------------------------
If you have any questions regarding ParsEval, feel free to contact the authors
using the ParsEval mailing list (parseval-users@lists.sourceforge.net) or by
direct email (daniel.standage@gmail.com).